Contacts of the strand formed by residues 166 - 174 (chain C) in PDB entry 1XHU


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ILE 166 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  LEU*     5.3     2.5    -      -       +      -
    112C  THR*     5.1     7.4    -      -       +      +
    113C  ALA*     5.4     1.6    -      -       +      -
    125C  LEU*     3.1    44.9    -      -       +      +
    127C  ASP*     5.8     1.1    -      -       +      -
    143C  ILE*     5.0     8.1    -      -       +      -
    148C  LEU*     4.2    12.6    -      -       +      -
    151C  THR*     5.2     3.6    -      -       +      -
    164C  PHE*     4.8     4.7    -      -       +      -
    165C  ASP*     1.3    71.0    -      -       -      +
    167C  ASN*     1.3    60.6    +      -       -      +
    168C  TYR*     3.5    22.4    -      -       +      +
    190C  LEU*     3.0    51.8    +      -       +      +
    191C  PHE*     3.3    28.7    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 167 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  SER*     4.2     6.7    -      -       -      +
    124C  GLU*     2.7    41.4    +      -       +      +
    125C  LEU      2.8     9.2    +      -       -      +
    126C  LEU*     4.3     8.5    -      -       +      -
    127C  ASP*     3.0    22.9    +      -       -      +
    165C  ASP*     3.6    13.1    +      -       -      +
    166C  ILE*     1.3    76.7    -      -       -      +
    168C  TYR*     1.3    74.0    +      -       -      +
    187C  PHE*     3.5    29.3    -      -       +      -
    188C  ALA      3.7     2.9    -      -       -      +
    189C  GLU*     3.4    28.8    +      -       -      +
    191C  PHE*     5.7     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 168 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127C  ASP*     3.3    33.9    -      -       +      +
    129C  LYS*     3.5    22.2    -      -       +      -
    142C  ILE*     3.2    35.4    -      -       +      -
    143C  ILE*     3.0    33.6    -      -       +      +
    166C  ILE*     3.5    23.1    -      -       +      +
    167C  ASN*     1.3    78.8    -      -       -      +
    169C  LEU*     1.3    60.3    +      -       -      +
    187C  PHE*     3.7     3.7    -      -       -      -
    188C  ALA*     3.2    20.7    +      -       +      +
    190C  LEU*     3.5    36.7    -      -       +      +
    210C  PHE*     4.5    10.8    -      +       +      -
    212C  VAL*     3.0    26.7    -      -       +      +
    215C  LEU*     5.9     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 169 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  ILE*     4.9     7.4    -      -       +      -
      8C  TYR*     3.5    20.6    -      -       +      -
     11C  ILE*     4.8     8.1    -      -       +      -
     15C  LEU*     4.8     4.3    -      -       +      -
     41C  VAL*     3.6    39.5    -      -       +      -
     45C  LEU*     6.5     0.2    -      -       +      -
    126C  LEU*     4.2    13.6    -      -       +      +
    127C  ASP      2.7    13.3    +      -       -      +
    128C  VAL*     3.2     9.7    -      -       +      +
    129C  LYS      2.8    24.8    +      -       -      -
    168C  TYR*     1.3    73.0    -      -       -      +
    170C  GLU*     1.3    62.5    +      -       -      +
    171C  VAL*     4.7     3.1    -      -       +      -
    185C  THR*     3.3    32.8    -      -       +      -
    186C  SER      3.6     9.4    -      -       -      +
    187C  PHE*     3.9     9.4    -      -       +      -
    212C  VAL*     4.4     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 170 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129C  LYS*     3.2    17.7    -      -       -      +
    131C  ARG*     2.9    34.7    +      -       +      +
    169C  LEU*     1.3    72.1    -      -       -      +
    171C  VAL*     1.3    63.6    +      -       -      +
    172C  ASP*     2.9    30.8    -      -       -      +
    185C  THR*     3.2    29.3    -      -       -      +
    186C  SER*     2.7    20.9    +      -       -      +
    211C  HIS*     3.9     1.9    -      -       -      -
    212C  VAL*     2.8    51.6    +      -       +      +
    213C  ARG*     2.9    10.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 171 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  LEU*     5.0     9.2    -      -       +      -
     37C  PHE*     3.9    33.0    -      -       +      -
     41C  VAL*     4.1    19.3    -      -       +      -
    128C  VAL*     3.5    26.0    -      -       +      -
    129C  LYS      3.1     9.1    +      -       -      -
    130C  THR*     3.5    20.3    -      -       +      -
    169C  LEU*     4.4     5.6    -      -       +      +
    170C  GLU*     1.3    79.2    -      -       -      +
    172C  ASP*     1.3    60.8    +      -       -      +
    173C  TRP*     3.4    16.1    -      -       -      -
    182C  CYS*     4.1    20.4    -      -       +      -
    184C  SER      4.0     2.0    -      -       -      -
    185C  THR*     5.1     0.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 172 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131C  ARG*     3.6    20.6    +      -       -      +
    133C  ILE*     5.2     7.5    -      -       +      +
    170C  GLU*     2.9    32.0    -      -       -      +
    171C  VAL*     1.3    70.9    -      -       -      +
    173C  TRP*     1.3    55.4    +      -       -      +
    182C  CYS*     3.0     7.3    -      -       -      -
    183C  VAL*     2.6    36.5    +      -       +      -
    184C  SER*     2.9    47.2    +      -       -      +
    185C  THR*     3.8     3.1    +      -       -      -
    186C  SER*     5.0     0.5    +      -       -      -
    213C  ARG*     4.7    10.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 173 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28C  LEU*     3.4    33.7    -      -       +      -
     33C  ALA*     4.1    18.4    -      -       +      -
     34C  GLY      4.3     2.5    -      -       -      +
     37C  PHE*     3.4    26.7    -      +       +      -
    130C  THR*     3.8    19.2    +      -       -      -
    131C  ARG      3.1    29.4    +      -       -      +
    132C  ASN*     3.0    34.9    -      -       +      -
    133C  ILE*     3.1    27.5    +      -       -      +
    171C  VAL      3.4    12.8    -      -       -      -
    172C  ASP*     1.3    75.1    -      -       -      +
    174C  GLU*     1.3    77.1    +      -       -      +
    175C  LEU*     4.0    10.5    -      -       -      -
    180C  LEU*     3.4    40.8    -      -       +      -
    181C  VAL      3.1    15.9    -      -       -      +
    183C  VAL*     4.4     1.6    -      -       -      +
     10L    C      4.7     1.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 174 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  ASN*     4.5     4.0    -      -       -      -
    133C  ILE*     3.6    19.2    -      -       +      +
    134C  SER*     4.7     8.7    -      -       -      +
    173C  TRP*     1.3    81.1    -      -       -      +
    175C  LEU*     1.3    56.2    +      -       -      +
    176C  ASN*     2.6    36.3    +      -       +      +
    181C  VAL*     3.2    19.5    +      -       +      +
    183C  VAL*     3.9    23.6    -      -       +      +
----------------------------------------------------------
 Back to top of page


A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il